Lossless compression of FASTQ, BAM, VCF
2x - 10x better than .gz / .cram

Name: Genozip Limited
Address: HK

The world's best lossless compressor for FASTQ, BAM, VCF in a wide variety of use cases

Used in hundreds of institutions, research hospitals, and companies

NEW! Compress a FASTQ file in ½ time with a little help from its BAM

If you have both FASTQ and BAM files available and want to compress both - well, that's what Genozip Deep™ is for. But what if you only want to compress the FASTQs and not the BAMs?

With the new BAM-Assisted Compression of FASTQ method (patent pending), Genozip can now inspect the BAM ahead of compressing the related FASTQs, using the alignment data from the BAM to slash the compression time of the FASTQ in half, while also modestly improving the compression ratio.

Available in Genozip version 15.0.69

CPU consumption without (blue) and with BAM-Assist (orange), when compressing whole-genome sequencing FASTQs

New! Genozip Deep™ (patent pending)
Co-compression of FASTQ and BAM

Need to compress both FASTQ and BAM files? By co-compressing them together, Genozip Deep™ takes advantage of the information overlap between the FASTQ and BAM data to dramatically shrink the compressed file size. When uncompressing, the FASTQ and BAM files are recovered precisely.

Available in Genozip version 15.0.4

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Read our FASTQ+BAM
co-compression pre-print

Columbia University, Institute of Genomic Medicine

Daniel S. T. Hughes, Director of Bioinformatics

"The Institute of Genomic Medicine's (IGM) Bioinformatics Core, situated within the Columbia University Irving School of Medicine, manages a variant warehouse containing approximately 130,000 whole-genome sequencing (WGS) and whole-exome sequencing (WES) samples. This warehouse serves the dual purpose of gene discovery and diagnostic analysis and has been utilized in numerous published analyses. Additionally, the IGM acts as a long-term repository for original off-machine FASTQ files of internally and externally sequenced samples, which must be preserved in their original form.

After an extensive evaluation of the cost, compute, compression benefits of multiple options we decided upon the use of Genozip Premium package.

We applied the lossless Genozip compression on approximately 172,000 of our most recent internally stored FASTQ pairs. This reduced their data footprint from 537.4 TB to 115.6 TB, resulting in an average space savings of 78.5%. Not only did this significantly reduce storage costs, but it also facilitated the migration of the entire dataset to our cloud infrastructure.

I can highly recommend Genozip to any organization looking to reduce the storage footprint of their FASTQ files."

Lille University Hospital Center

Bioinformatics Team

"At Lille University Hospital Center, we regularly manage massive volumes of genomic data. These data require significant storage capacities and efficient management for routine operations.

Since we have started using Genozip, our way of handling genomic data has radically changed. Its ultra-efficient compression technology has allowed us to significantly reduce the digital footprint of our files, often by more than 60%, while maintaining impeccable data quality. This has already led to the freeing up of more than 200 TB of genomic data.

With Genozip, we have seen a significant reduction in costs associated with data storage. For any organization that deals with large amounts of genomic data, we highly recommend Genozip. It is an essential tool that optimizes storage space and improves the efficiency of genomic data management operations."

James Bonfield

Co-developer of CRAM in samtools and current maintainer of the CRAM specification

"Use Genozip if you want a commercial alternative to CRAM" (Personal opinion posted on X)

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